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BP_FIND-BLAST-MATCHES(1p) User Contributed Perl Documentation BP_FIND-BLAST-MATCHES(1p)

NAME - extract DNA sequences based on BLAST hits

SYNOPSIS [-h -e -p -5 -n -o -3 -header] -blast <BLAST_FILE> -fasta <FASTA_FILE>



BLAST output file to read from. The alignment should use the file specified by '-fasta' option ideally
FASTA file to read from. This is where the sequence will be extracted from


Displays this help message
Maximum e-value for matches (0.01 by default)
Number of base pairs of 5' region to be included with the sequence
Number of base pairs of 5' region only, excluding the regular sequence
Number of base pairs of 3' region only, excluding the regular sequence
Number of top hits to display, starting with the best hit
Exact match to display (this option can't be used in conjunction with '-n'
The FASTA header to display instead of the default


This script takes a BLAST output file and a FASTA file as arguments, given after the '-blast' and '-fasta' options respectively. The BLAST output file should have been generated with your sequence of interest and the FASTA file supplied as an argument. Example: -blast BLAST_FILE -fasta FASTA_FILE

It parses through the BLAST file to check for high quality matches, which are then searched for in the FASTA file. The sequence may vary from you candidate sequence, hence the BLAST search prior.

The sequence from the FASTA file is then displayed to STDOUT. Optional arguments can be used, such as to extract the 5' or 3' region.


Gabriel Abud - <>


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2014-08-04 - Gabriel Abud
First features added


Getopt::long, Pod::Usage, Bio::SearchIO, Bio::Seq, Bio::SeqIO, File::Basename

2020-10-28 perl v5.30.3